Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers

One of the challenges in protein interaction studies with chemical cross-linking stems from the complexity of intra-, inter-, and dead-end cross-linked peptide mixtures. We have developed new cross-linkers to study protein-protein interactions with mass spectrometry to improve the ability to deal with this complexity. Even the accurate mass capabilities of FTICR-MS alone cannot unambiguously identify cross-linked peptides from cell-labeling experiments due to the complexity of these mixtures resultant from the enormous number of possible cross-linked species. We have developed novel cross-linkers that have unique fragmentation features in the gas phase. The characteristics of these cross-linkers combined with the accurate mass capability of FTICR-MS can help distinguish cross-linking reaction products and assign protein identities. These cross-linkers that we call protein interaction reporters (PIRs) have been constructed with two reactive groups attached through two bonds that can be preferentially cleaved by low-energy CID of the respective protonated precursor ions. After cleavage of the labile bonds, the middle part of the linker serves as a reporter ion to aid identification of cross-linked peptides. This report highlights three new PIRs with new features that have been developed to improve the efficiency of release of reporter ions. The new cross-linkers reported here were tuned with the addition of an affinity tag, a hydrophilic group, a photocleavable group, and new low-energy MS/MS cleavable bonds. This report presents our investigation of the MSMS fragmentation behavior of selected protonated ions of the new compounds. The comprehensive fragmentation of these PIRs and PIR-labeled cross-linked peptides with low-energy collisions and an example of electron capture dissociation in FTICR-MS is presented. These new cross-linkers will contribute to current systems biology research by allowing acquisition of global or large-scale data on protein-protein interactions.     

Relative dissociation energies of protonated peptides by electrospray ionization/surface-induced dissociation

Relative dissociation energies (RDEs) are obtained for the major fragment ions produced by electrospray ionization/surface-induced dissociation of singly protonated triglycine, tetraglycine, leucine enkephalin, and leucine enkephalin arginine. A previously described data analysis method (Lim, H.; et al. J. Phys. Chem. B 1998, 102, 4753) is employed to analyze the energy-resolved mass spectra by subtracting out the distribution of energy transferred to the surface, integrating over the distribution of the incident ion energy, and taking into account the precursor ion initial internal energy and kinetic energy distributions. These variables are optimized by anchoring the RDE for the lowest energy fragment of a given precursor ion to its literature values and then using these optimized parameters to obtain the other RDEs. The RDEs of the four major fragments of triglycine vary from 2.4 eV for the b(2) fragment ion to 6.0 eV for the a(2) ion. The RDEs of the four major fragments of tetraglycine vary from 3.2 eV for the y(2) ion to 5.7 eV for the a(2) ion. The leucine enkephalin RDEs range from 1.1 eV for the b(4) ion to 2.1 eV for the b(2) ion. The leucine enkephalin arginine RDEs all lay between 2.5 and 3.5 eV. The overall trend of fragmentation order for all peptides is (y(n), b(n)) < a(n) and is consistent with the results from other experiments. The peptide RDEs presented here are only as accurate as the literature values to which they are anchored. Determination of absolute dissociation energies from SID data will require further refinement of the data analysis method.     

Supercharged protein and peptide ions formed by electrospray ionization

The multiple charging of large molecules in electrospray ionization provides key advantages for obtaining accurate molecular weights by mass spectrometry and for obtaining structural information by tandem mass spectrometry and MS(n) experiments. Addition of glycerol or m-nitrobenzyl alcohol into the electrospray solutions dramatically increases both the maximum observed charge state and the abundances of the high charge states of protein and peptide ions. Adding glycerol to acidified aqueous solutions of cytochrome c shifts the most abundant charge state from 17+ to 21+, shifts the maximum charge state from 20+ to 23+, and shifts the average charge state from 16.6+ to 20.9+. Much less m-nitrobenzyl alcohol (<1%) is required to produce similar results. With just 0.7% m-nitrobenzyl alcohol, even the 24+ charge state of cytochrome c is readily observed. Similar results are obtained with myoglobin and (Lys)4. For the latter molecule, the 5+ charge state is observed in the electrospray mass spectrum obtained from solutions containing 6.7% m-nitrobenzyl alcohol. This charge state corresponds to protonation of all basic sites in this peptide. Although the mechanism for enhanced charging is unclear, it does not appear to be a consequence of conformational changes of the analyte molecules. This method of producing highly charged protein ions should be useful for improving the performance of mass measurements on mass spectrometers with performances that decrease with increasing m/z. This should also be particularly useful for tandem mass spectrometry experiments, such as electron capture dissociation, for which highly charged ions are desired.     

Determination of dissociation constants for protein-ligand complexes by electrospray ionization mass spectrometry

A fully automated biophysical assay based on electrospray ionization mass spectrometry (ESI-MS) for the determination of the dissociation constants (KD) between soluble proteins and low molecular mass ligands is presented. The method can be applied to systems where the relative MS response of the protein and the protein-ligand complexes do not reflect relative concentrations. Thus, the employed approach enables the use of both electrostatically and nonpolar bound complexes. The dynamic range is wider than for most biological assays, which facilitates the process of establishing a structure-activity relationship. This fully automated ESI-MS assay is now routinely used for ligand screening. The entire procedure is described in detail using hGHbp, a 25-kDa extracellular soluble domain of the human growth hormone receptor, as a model protein.     

Electron-transfer reagent anion formation via electrospray ionization and collision-induced dissociation

A strategy is described and demonstrated for the formation of reagent anions via electrospray ionization (ESI) for electron-transfer dissociation (ETD). To circumvent difficulties associated with formation of high mass-to-charge ratio (m/z) reagent anions, it is desirable to form ETD reagents via means other than those that require reagent molecule vaporization. ESI is a candidate method, but anions that are generally generated efficiently by ESI tend to react with multiply protonated polypeptides via proton transfer. The strategy described herein involves the use of a precursor reagent molecule that ionizes efficiently via electrospray ionization and that can subsequently be converted to an ETD reagent via gas-phase dissociation. The approach is demonstrated with arenecarboxylic acids that yield strong signals associated with the deprotonated molecule and that subsequently undergo collision-induced dissociation (CID) by loss of CO(2). In the present work, triply protonated KGAILKGAILR served as a test substrate for the CID product ions to give rise to ETD. Several precursor molecules were shown to be capable of generating ETD reagents via ESI followed by CID. These included 9-anthracenecarboxylic acid, 2-fluoro-5-iodobenzoic acid, and 2-(fluoranthene-8-carbonyl)benzoic acid. The latter molecule has the most attractive set of characteristics as a precursor for a relatively high m/z ratio ETD reagent.     

Electrothermal supercharging of proteins in native electrospray ionization

The formation of high charge-state protein ions with nanoelectrospray ionization (nESI) from purely aqueous ammonium bicarbonate solutions at neutral pH, where the proteins have native or native-like conformations prior to ESI droplet formation, is demonstrated. This "electrothermal" supercharging method depends on the temperature of the instrument entrance capillary, the nESI spray potential, and the solution ionic strength and buffer, although other factors almost certainly contribute. Mass spectra obtained with electrothermal supercharging appear similar to those obtained from denaturing solutions where charging beyond the total number of basic sites can be achieved. For example, a 17+ ion of bovine ubiquitin was formed by nESI of a 100 mM ammonium bicarbonate, pH 7.0, solution, which is three more charges than the total number of basic amino acids plus the N-terminus. Heating of the ESI droplets in the vacuum/atmosphere interface and the concomitant denaturation of the protein in the ESI droplets prior to ion formation appears to be the primary origin of the very high charge-state ions formed from these purely aqueous, buffered solutions. nESI mass spectra resembling those obtained under traditional native or denaturing conditions can be reversibly obtained simply by toggling the spray voltage between low and high values.     

Structural analysis of polymer end groups by electrospray ionization high-energy collision-induced dissociation tandem mass spectrometry

Chemical structures of polymer end groups play an important role in determining the functional properties of a polymeric system. We present a mass spectrometric method for determining end group structures. Polymeric ions are produced by electrospray ionization (ESI), and they are subject to source fragmentation in the ESI interface region to produce low-mass fragment ions. A series of source-fragment ions containing various numbers of monomer units are selected for high-energy collision-induced dissociation (CID) in a sector/time-of-flight tandem mass spectrometer. It is shown that high-energy CID spectra of source-induced fragment ions are very informative for end group structure characterization. By comparing the CID spectra of fragment ions with those of known chemicals, it is possible to unambiguously identify the end group structures. The utility of this technique is illustrated for the analysis of two poly(ethylene glycol)-based slow-releasing drugs where detailed structural characterization is of significance for drug formulation, quality control, and regulatory approval. Practical issues related to the application of this method are discussed.     

Multiply charged negative ions by electrospray ionization of polypeptides and proteins.

Multiply deprotonated polypeptide and protein molecules, (M - nH)n-, produced from pH approximately 11 aqueous solutions, are analyzed by electrospray ionization-mass spectrometry (ESI-MS). Aqueous ammonium hydroxide solutions of the analyte are shown to be preferable to sodium hydroxide solutions for negative-ion ESI due to the production of multiply sodiated protein species from the latter system. Proteins with Mr to 66,000 and having up to 57 negative charges have been detected. Multiply charged negative ions can be produced from ESI of the highly acidic protein pepsin (Mr approximately 34,600) because of its relatively large number of acidic residues, 42. In contrast, the small number of basic amino acid residues for pepsin (4) does not allow formation of highly protonated species essential for positive-ion detection, for mass spectrometers of limited m/z range. Similarly, negative-ion ESI-MS is extended to large oligosaccharide analysis. Preliminary tandem mass spectrometry experiments of multiply charged polypeptide anions demonstrate the utility and potential of negative-ion ESI-MS for structural elucidation.     

Mass spectrometric behavior of thiazide-based diuretics after electrospray ionization and collision-induced dissociation

The mass spectrometric behavior of 21 thiazide-based compounds after electrospray ionization in the negative ion mode and collision-induced dissociation was investigated on a triple-stage quadrupole mass spectrometer. The mass spectra show individual and common fragmentation patterns, the generations of which are discussed based on comparable molecular structures of commercially available substances and the synthesis of unlabeled, deuterated, and 15N-labeled analogues. The synthesis of deuterated thiazides is perfomed by condensation of 4-amino-6-chloro-1,3-benzenedisulfonamide with appropriately labeled aldehydes, while the introduction of 15N into the sulfonamide groups of thiazides was achieved by the synthesis of 4-amino-6-chloro-1,3-benzenedisulfonamide(15N2) from 3-chloroaniline via 4-amino-6-chloro-1,3-benzenedisulfonyl chloride. The most common fragments determined are m/z 269, 205, and 126 for 6-chloro-7-sulfamoyl-3-alkyl-3,4-dihydro-1,2,4-benzothiadiazine-1,1-dioxides and m/z 303, 239, and 160 for 6-trifluoromethyl-7-sulfamoyl-3-alkyl-3,4-dihydro-1,2,4-benzothiadiazine-1,1-dioxides. Individual fragmentation behaviors were found that mainly depended on the C-3-linked side chain.     

Direct ionization of large proteins and protein complexes by desorption electrospray ionization-mass spectrometry

Desorption electrospray ionization-mass spectrometry (DESI-MS) has advantages for rapid sample analysis with little or no sample pretreatment, but performance for large biomolecules has not been demonstrated. In this study, liquid sample DESI, an extended version of DESI used for analysis of liquid samples, was shown to have capabilities for direct ionization of large noncovalent protein complexes (>45 kDa) and proteins (up to 150 kDa). Protein complex ions (e.g., superoxide dismutase, enolase, and hemoglobin) desorbed from solution by liquid sample DESI were measured intact, indicating the capability of DESI for preserving weak noncovalent interactions. Doping the DESI spray solvent with supercharging reagents resulted in protein complex ions having increased multiple charging without complex dissociation. Ion mobility measurements of model protein cytochrome c showed that the supercharging reagent favored the more compact conformation for the lower charged protein ions. Liquid sample DESI of hydrophobic peptide gramicidin D suggests that the ionization mechanism involves a droplet pick-up mixing process. Measurement of liquid samples significantly extends the mass range of DESI-MS, allowing the analysis of high-mass proteins such as 150 kDa immunoglobulin G (IgG) and thus represents the largest protein successfully ionized by DESI to date.     

Charge-surface correlation in electrospray ionization of folded and unfolded proteins

Electrospray-ionization mass spectrometry (ESI-MS) is widely used for protein studies. It has been shown that the extent of protein ionization under nondenaturing conditions correlates well with the solvent-accessible surface area of the tridimensional structure, for either folded monomers or multimeric complexes. The goal of this study was to test whether this relation holds for unfolded proteins as well. In order to overcome the paucity of structural data, the server ProtSA was used to model the conformational ensembles of proteins in the unfolded state and generate estimates of the average solvent accessibility. The results are analyzed along with literature data or original measurements by ESI-MS. It is found that the charge-to-surface relation holds for proteins in the unfolded state, free from solvent effects. A double-log plot is derived, in close agreement with published data for folded proteins. These results suggest that the solvent-accessible surface area is a key factor determining the extent of protein ionization by electrospray, independent of the conformational state. This conclusion helps rationalizing conformational effects in protein ESI-MS. The here reported relation can be used to predict the average solvent accessibility and, hence, the state of folding of unknown proteins from ESI-MS data.     

Effect of reducing disulfide-containing proteins on electrospray ionization mass spectra

Electrospray ionization produces multiply charged molecular ions for biomolecules with molecular weights in excess of 100,000. This allows mass spectrometers with limited mass-to-charge range to extend their molecular weight range by a factor equal to the number of charges. The maximum number of observed charges for peptides and smaller proteins correlates well with the number of basic amino acid residues (Arg, Lys, His), except for disulfide-containing molecules, such as lysozyme and bovine albumin. However, reduction of disulfide linkages with 1,4-dithiothreitol (Cleland's reagent) may allow the protein to be in an extended conformation and make "buried" basic residues available for protonation to yield higher charged molecular ions by the electrospray ionization process. For larger proteins reduction of disulfide bridges greatly increases the maximum charge state, but charging of basic amino acid residues remains less efficient than for smaller proteins.     

On the formation of highly charged gaseous ions from unfolded proteins by electrospray ionization

Electrospray ionization (ESI) of native proteins results in a narrow distribution of low protonation states. ESI for these folded species proceeds via the charged residue mechanism. In contrast, ESI of unfolded proteins yields a wide distribution of much higher charge states. The current work develops a model that can account for this effect. Recent molecular dynamics simulations revealed that ESI for unfolded polypeptide chains involves protein ejection from nanodroplets, representing a type of ion evaporation mechanism (IEM). We point out the analogies between this IEM, and the dissociation of gaseous protein complexes after collisional activation. The latter process commences with unraveling of a single subunit, in concert with Coulombically driven proton transfer. The subunit then separates from the residual complex as a highly charged ion. We propose that similar charge equilibration events accompany the IEM of unfolded proteins, thereby causing the formation of high ESI charge states. A bead chain model is used for examining how charge is partitioned as protein and droplet separate. It is shown that protein ejection from differently sized ESI droplets generates a range of protonation states. The predicted behavior agrees well with experimental data.     

Conformational and noncovalent complexation changes in proteins during electrospray ionization

Electrospray ion sources efficiently produce gas-phase ions from proteins and their noncovalent complexes. Charge-state distributions of these ions are increasingly used to gauge their conformations in the solution phase. Here we investigate how this correlation is affected by the spraying conditions at the early stage of droplet generation, prior to the ionization process. We followed the folding behavior of model proteins cytochrome c and ubiquitin and the dissociation of the noncovalent holomyoglobin complex. Spray current measurements, fast Taylor cone imaging, and mass analysis of the generated ions indicated that the protein structure experienced conformational or complexation changes upon variations in the spraying mode of the electrospray ionization source. These effects resulted in a departure from the original secondary, tertiary, and quaternary structure of proteins, possibly introducing artifacts in related studies. Therefore, if a particular gas-phase ion conformation is required or correlations with the liquid-phase conformations are studied, it is advantageous to maintain a particular spraying mode. Alternatively, spraying mode-induced changes can be utilized to alter the structure of proteins in, for example, time-resolved experiments for the study of protein folding dynamics.     

In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry

Enhanced charging, or supercharging, of analytes in electrospray ionization mass spectrometry (ESI MS) facilitates high resolution MS by reducing an ion mass-to-charge (m/z) ratio, increasing tandem mass spectrometry (MS/MS) efficiency. ESI MS supercharging is usually achieved by adding a supercharging reagent to the electrospray solution. Addition of these supercharging reagents to the mobile phase in liquid chromatography (LC)-MS/MS increases the average charge of enzymatically derived peptides and improves peptide and protein identification in large-scale bottom-up proteomics applications but disrupts chromatographic separation. Here, we demonstrate the average charge state of selected peptides and proteins increases by introducing the supercharging reagents directly into the ESI Taylor cone (in-spray supercharging) using a dual-sprayer ESI microchip. The results are comparable to those obtained by the addition of supercharging reagents directly into the analyte solution or LC mobile phase. Therefore, supercharging reaction can be accomplished on a time-scale of ion liberation from a droplet in the ESI ion source.     

On-line electrodialytic salt removal in electrospray ionization mass spectrometry of proteins

Salts and buffers, commonly used in isolation and stabilization of biological analytes, have a deleterious effect on electrospray ionization mass spectrometry (ESI-MS). Excessive concentrations of salts lead to ion suppression and adduct formation, which mask or complicate ion signals. In this work, we describe a salt remover (SR), configured as a three-compartment flow-through system, where the central compartment is separated from the outer compartments by a cation-exchange membrane (CEM) and an anion-exchange membrane (AEM). One platinum electrode is placed in each of the outer compartments, where water or electrolyte is flowing. The CEM electrode is held at a negative potential relative to the AEM side; cations/anions migrate by electrophoresis to the CEM/AEM receiver liquids, respectively. Proteins have poorer electrophoretic mobility relative to the buffer components, permitting removal of the salt. The salt-free proteins proceed to the ESI source. The capillary scale SR (internal volume 2.5 μL) described here effectively desalted continuous flows of NaCl solutions (200 mequiv/L at 1 μL/min, equivalent to a flux of 200 nequiv/min with 88% efficiency) and achieved >99.8% salt removal with 154 mM NaCl (isotonic saline) at 1 μL/min. With optimized current, >80% of concurrently present 20 μM protein was transmitted. Desalting efficiency and analyte loss was evaluated with different salt concentration and flow rate combinations under different applied current. Good-quality ESI-MS spectra of cytochrome c, myoglobin, and lysozyme as test proteins in a saline solution, passed through the SR, are demonstrated.     

Desorption electrospray ionization of explosives on surfaces: sensitivity and selectivity enhancement by reactive desorption electrospray ionization

Desorption electrospray ionization (DESI), an ambient mass spectrometry technique, is used for trace detection of the explosives trinitrohexahydro-1,3,5-triazine (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 2,4,6-trinitrotoluene (TNT), Pentaerythritol tetranitrate (PETN), and their plastic compositions (Composition C-4, Semtex-H, Detasheet) directly from a wide variety of surfaces (metal, plastic, paper, polymer) without sample preparation or pretreatment. Analysis of the explosives is performed under ambient conditions from virtually any surface in very short times (<5 s) including confirmatory tandem mass spectrometry (MS/MS) experiments, while retaining the sensitivity and specificity that mass spectrometry offers. Increased selectivity is obtained both by MS/MS and by performing additional experiments in which additives are included in the spray solvent. These reactive DESI experiments (reactions accompanying desorption) produce such ions as the chloride and trifluoroacetate adducts of RDX and HMX or the Meisenheimer complex of TNT. Desorption atmospheric pressure chemical ionization, a variant of DESI that uses gas-phase ions generated by atmospheric pressure corona discharges of toluene or other organic compounds, provides evidence for a heterogeneous-phase (gaseous ion/absorbed analyte) charge-transfer mechanism of DESI ionization in the case of explosives. Plastic explosives on surfaces were analyzed directly as fingerprints, without sample preparation, to test DESI as a possible method for in situ detection of explosives-contaminated surfaces. DESI also allowed detection of explosives in complex matrixes, including lubricants, household cleaners, vinegar, and diesel fuel. Absolute limits of detection for the neat explosives were subnanogram in all cases and subpicogram in the case of TNT. The DESI response was linear over 3 orders of magnitude for TNT. Quantification of RDX on paper gave a precision (RSD) of 2.3%. Pure water could be used as the spray solution for DESI, and it showed ionization efficiencies for RDX in the negative ion mode similar to that given by methanol/water. DESI represents a simple and rapid way to detect explosives in situ with high sensitivity and specificity and is especially useful when they are present in complex mixtures or in trace amounts on ordinary environmental surfaces.     

Enhancing electrospray ionization efficiency of peptides by derivatization

With the advent of electrospray ionization mass spectrometry, the world was given a new way to look at complex peptide mixtures. Identification of proteins via their signature peptides requires ionization of a representative portion of the peptides derived from proteins by proteolysis. Unfortunately, matrix effects prohibited electrospray ionization of many peptides. This paper describes the development of a new labeling reagent that simultaneously adds a permanent positive charge to peptides and increases their hydrophobicity to enhance their ionization efficiency. The labeling agent is preactivated with N-hydroxysuccinimide to react with primary amines to form a peptide bond. In the most dramatic case, ionization efficiency of the peptide ADRDQYELLCLDNTRKPVDEYK increased 500-fold after derivatization as opposed to other peptides where ionization efficiency was impacted little. Ionization efficiency of peptides was enhanced roughly 10-fold in general by derivatization. Peptides of less than 500 Da experienced the greatest increase in ionization efficiency by derivatization. Poor ionization efficiency of native peptides was found to be due more to their inherent structural properties than the matrix in which ionization occurs.     

Characterization of archaeological beeswax by electron ionization and electrospray ionization mass spectrometry

To better detect and identify beeswax in ancient organic residues from archaeological remains, we developed a new analytical methodology consisting of the analysis of (i) the trimethylsilylated organic extract by GC/MS and (ii) the crude extract by ESI-MS. Selective scanning modes, such as SIM or MRM, permit separate quantification of each chemical family (fatty acids, monoesters, monohydroxyesters, and diesters) and allow an improvement in sensitivity and selectivity, allowing the crude extract to be treated without further purification. GC/MS (SIM) was revealed to be a powerful method for the detection of components, with a detection limit down to a total lipid extract in the range of approximately 50 ng in a complex matix, such as archaeological degraded material, whereas ESI-MS/MS is instead used for the detection of nonvolatile biomarkers. Identification by GC/MS (SIM) and ESI-MS/ MS (MRM) of more than 50 biomarkers of beeswax in an Etruscan cup at the parts-per-million level provides the first evidence for the use of this material by the Etruscans as fuel or as a waterproof coating for ceramics.     

Identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and LC ESI infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometry.

Here we propose a novel method for rapidly identifying proteins in complex mixtures. A list of candidate proteins (including provision for posttranslational modifications) is obtained by database searching, within a specified mass range about the accurately measured mass (e.g., +/- 0.1 Da at 10 kDa) of the intact protein, by capillary liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). On alternate scans, LC ESI infrared multiphoton dissociation (IRMPD) FT-ICR MS yields mostly b and y fragment ions for each protein, from which the correct candidate is identified as the one with the highest "hit" score (i.e., most b and y fragments matching the candidate database protein amino acid sequence masses) and sequence "tag" score (based on a series of fragment sequences differing in mass by 1 or 2 amino acids). The method succeeds in uniquely identifying each of a mixture of five proteins treated as unknowns (melittin, ubiquitin, GroES, myoglobin, carbonic anhydrase II), from more than 1000 possible database candidates within a +/- 500 Da mass window. We are also able to identify posttranslational modifications of two of the proteins (mellitin and GroES). The method is simple, rapid, and definitive and is extendable to a mixture of affinity-selected proteins, to identify proteins with a common biological function.